Exploring the Mechanics of Gene Expression

New NSF grant links four Duke engineers to explore how mechanical changes to genetic material affects gene expression, cancer development

An artistic rendition of the epigenome controlling the

A team of engineers at Duke University have secured a four-year, $2 million “Emerging Frontiers” grant from the National Science Foundation to explore how structural changes to DNA affect gene regulation, as well as the downstream implications for cellular processes such as tumor development.

The project capitalizes on varied strengths across engineering at Duke University, from gene editing to mechanical engineering to computational modeling. At the heart of the project is technology developed by Charles Gersbach, the Rooney Family Associate Professor of Biomedical Engineering, that uses a variation of the genetic editing system CRISPR-Cas9 to precisely modulate the epigenome.

The epigenome includes all of the proteins, chemical modifications and other biomolecules that package, support, and control the expression of genes encoded by DNA. Our genomic DNA constitutes the blueprint for life, but the epigenome determines which parts are used, as well as where and when. Together, the molecules that make up our DNA and epigenome are referred to as chromatin.

“The complexity of human biology is determined not by how many genes we have, but rather how those genes are dialed up and down dynamically in different cell types and in response to different conditions,” said Gersbach. “The sequencing of the human genome has led to significant advances in our knowledge of gene function, but we still have a very poor understanding of how the control elements of our genome turn genes on and off. Manipulation of the epigenome with CRISPR-Cas9 technologies allows us to study these questions with precision that wasn’t previously possible.”

While the original CRISPR-Cas9 system locates and cuts specific sequences of DNA, Gersbach and his colleagues have engineered it to instead manipulate the epigenome adjacent to specific sequences.

In the new project, this technology will be used to introduce changes to the chromatin structure around the C-MYC gene, which is known to cause cells to become cancerous under certain conditions. To link the changes in chromatin structure to cancer progression, the team will take advantage of lab-grown human organoid technology developed by Xiling Shen, the Hawkins Family Associate Professor of Biomedical Engineering at Duke.

To better understand the underpinnings of these changes, the group will turn to both computer simulations and novel biosensors.

Michael Rubinstein, professor of mechanical engineering and materials science, biomedical engineering, chemistry, and physics at Duke, will computationally model the mechanical properties of the chromatin and how this affects molecular dynamics and gene expression.

Brenton Hoffman, assistant professor of biomedical engineering and cell biology at Duke, will develop technologies to directly monitor the changes to chromatin using another CRISPR-based system that places fluorescent molecules at specific points of the genome. These molecules brighten and dim depending on their distance from one another, providing a way to image the effect of programmed epigenetic changes on genome structure at the single-molecule scale in living cells.

“This combination of innovative approaches to model, image and manipulate chromatin structure and its role in complex processes like tumor development has the potential to dramatically catalyze our fundamental understanding of biology,” added Gersbach. “It is a testament to the interdisciplinary and collaborative nature across the Pratt School of Engineering.”

The grant is one of eight projects recently awarded a total of $16 million for research to characterize the regulation of gene activity and expression, and to create strategies to modify those processes without altering the DNA sequence.

Supported by the NSF Directorate for Engineering's Emerging Frontiers in Research and Innovation (EFRI) program, and co-funded by the Biological Sciences Directorate and Mathematical and Physical Sciences Directorate, the awards signal a major investment in engineering biology and align with one of NSF's 10 Big Ideas for long-term discovery and innovation, Understanding the Rules of Life: Predicting Phenotype. Established in 2007, the EFRI program seeks to inspire and enable researchers to expand the limits of knowledge in the service of grand engineering challenges and national needs.